zzh
/
gatk-3.8
1
0
Fork 0
Code Issues Pull Requests Packages Projects Releases Wiki Activity

When you commit code late at night you tend to make careless mistakes... like forgetting to update integration tests. 

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4658 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
ebanks 2010-11-12 14:41:10 +00:00
parent 988da428ae
commit b51762c279
3 changed files with 12 additions and 12 deletions
Show Stats Download Patch File Download Diff File Expand all files Collapse all files

4
java/test/org/broadinstitute/sting/gatk/walkers/annotator/VariantAnnotatorIntegrationTest.java
View File

@ -31,7 +31,7 @@ public class VariantAnnotatorIntegrationTest extends WalkerTest {
public void testHasAnnotsAsking1() {
WalkerTestSpec spec = new WalkerTestSpec(
baseTestString() + " -G \"Standard\" -B:variant,VCF " + validationDataLocation + "vcfexample2.vcf -I " + validationDataLocation + "low_coverage_CEU.chr1.10k-11k.bam -L 1:10,020,000-10,021,000", 1,
Arrays.asList("bcd5c80e54d90f1ddf65e0c47b0710a5"));
Arrays.asList("a7680de85e0b118415bcd032b3b49688"));
executeTest("test file has annotations, asking for annotations, #1", spec);
}
@ -63,7 +63,7 @@ public class VariantAnnotatorIntegrationTest extends WalkerTest {
public void testNoAnnotsAsking1() {
WalkerTestSpec spec = new WalkerTestSpec(
baseTestString() + " -G \"Standard\" -B:variant,VCF " + validationDataLocation + "vcfexample2empty.vcf -I " + validationDataLocation + "low_coverage_CEU.chr1.10k-11k.bam -L 1:10,020,000-10,021,000", 1,
Arrays.asList("10ceed55fd51f104d4b57aa555770253"));
Arrays.asList("207a5af3647f1f0769fdd4dd6bd0c132"));
executeTest("test file doesn't have annotations, asking for annotations, #1", spec);
}

4
java/test/org/broadinstitute/sting/gatk/walkers/beagle/BeagleIntegrationTest.java
View File

@ -41,7 +41,7 @@ public class BeagleIntegrationTest extends WalkerTest {
"-B:beagleR2,BEAGLE " + beagleValidationDataLocation + "inttestbgl.r2 " +
"-B:beagleProbs,BEAGLE " + beagleValidationDataLocation + "inttestbgl.gprobs " +
"-B:beaglePhased,BEAGLE " + beagleValidationDataLocation + "inttestbgl.phased " +
"-o %s -NO_HEADER", 1, Arrays.asList("e04d9768cdb94d1f0e2e35a7f1bc49ab"));
"-o %s -NO_HEADER", 1, Arrays.asList("93546f4f6a7f5fe24f01a357dcad7c5f"));
executeTest("test BeagleOutputToVCF", spec);
}
@ -72,7 +72,7 @@ public class BeagleIntegrationTest extends WalkerTest {
"-B:beagleR2,beagle /humgen/gsa-hpprojects/GATK/data/Validation_Data/EUR_beagle_in_test.r2 "+
"-B:beagleProbs,beagle /humgen/gsa-hpprojects/GATK/data/Validation_Data/EUR_beagle_in_test.gprobs.bgl "+
"-B:beaglePhased,beagle /humgen/gsa-hpprojects/GATK/data/Validation_Data/EUR_beagle_in_test.phased.bgl "+
"-L 20:1-70000 -o %s -NO_HEADER ",1,Arrays.asList("fd104b7da9e6c99b662c6ad746fd53f3"));
"-L 20:1-70000 -o %s -NO_HEADER ",1,Arrays.asList("f8071eda9f762947c6a3404d6d126df2"));
executeTest("testBeagleChangesSitesToRef",spec);
}

16
java/test/org/broadinstitute/sting/gatk/walkers/variantutils/CombineVariantsIntegrationTest.java
View File

@ -60,21 +60,21 @@ public class CombineVariantsIntegrationTest extends WalkerTest {
}
@Test public void test1SNP() { test1InOut("pilot2.snps.vcf4.genotypes.vcf", "def6365e318cb506aa69ee8ec6899c4e"); }
@Test public void test2SNP() { test1InOut("pilot2.snps.vcf4.genotypes.vcf", "6d1d9fffcc10d4f9ab086760603b577e", " -setKey foo"); }
@Test public void test3SNP() { test1InOut("pilot2.snps.vcf4.genotypes.vcf", "e1d43e0c4df65df5e9761916b12f0b5b", " -setKey null"); }
@Test public void test1SNP() { test1InOut("pilot2.snps.vcf4.genotypes.vcf", "3287ddd7c5003b3c791048cb2532578a"); }
@Test public void test2SNP() { test1InOut("pilot2.snps.vcf4.genotypes.vcf", "1b8b58c2b231926f0ba45d29c5242df5", " -setKey foo"); }
@Test public void test3SNP() { test1InOut("pilot2.snps.vcf4.genotypes.vcf", "5aaa695bc1754d6abcbed27f0c0b4c64", " -setKey null"); }
@Test public void testOfficialCEUPilotCalls() { test1InOut("CEU.trio.2010_03.genotypes.vcf.gz", "79e7e474b0a2bb82930201f143328d5d"); } // official project VCF files in tabix format
@Test public void test1Indel1() { test1InOut("CEU.dindel.vcf4.trio.2010_06.indel.genotypes.vcf", "d93ee8b9f36eedc80a3afa548bffc888"); }
@Test public void test1Indel2() { test1InOut("CEU.dindel.vcf4.low_coverage.2010_06.indel.genotypes.vcf", "4d16ffe9cf3beff94ac05ea49f85049a"); }
@Test public void test1Indel2() { test1InOut("CEU.dindel.vcf4.low_coverage.2010_06.indel.genotypes.vcf", "26c99206407fb2c42beadcac5e5de246"); }
@Test public void combineTrioCalls() { combine2("CEU.trio.2010_03.genotypes.vcf.gz", "YRI.trio.2010_03.genotypes.vcf.gz", "", "78f2a2c09df8fa51ccfe5b3706a5e313"); } // official project VCF files in tabix format
@Test public void combineTrioCalls() { combine2("CEU.trio.2010_03.genotypes.vcf.gz", "YRI.trio.2010_03.genotypes.vcf.gz", "", "9b44bb39702b41240371815320e452d5"); } // official project VCF files in tabix format
@Test public void combineTrioCallsMin() { combine2("CEU.trio.2010_03.genotypes.vcf.gz", "YRI.trio.2010_03.genotypes.vcf.gz", " -minimalVCF", "460bdbeaf7e9641395ac2ce6e1afc106"); } // official project VCF files in tabix format
@Test public void combine2Indels() { combine2("CEU.dindel.vcf4.trio.2010_06.indel.genotypes.vcf", "CEU.dindel.vcf4.low_coverage.2010_06.indel.genotypes.vcf", "", "d445583e7f3a8bc98004e8e44878fce6"); }
@Test public void combine2Indels() { combine2("CEU.dindel.vcf4.trio.2010_06.indel.genotypes.vcf", "CEU.dindel.vcf4.low_coverage.2010_06.indel.genotypes.vcf", "", "02f0634d0176138e4195009eff7f2308"); }
@Test public void combineSNPsAndIndels() { combine2("CEU.trio.2010_03.genotypes.vcf.gz", "CEU.dindel.vcf4.low_coverage.2010_06.indel.genotypes.vcf", "", "e64284f598fc4f473ee5554282d84b0c"); }
@Test public void combineSNPsAndIndels() { combine2("CEU.trio.2010_03.genotypes.vcf.gz", "CEU.dindel.vcf4.low_coverage.2010_06.indel.genotypes.vcf", "", "d443358367211b96762ae64d1461b587"); }
@Test public void uniqueSNPs() { combine2("pilot2.snps.vcf4.genotypes.vcf", "yri.trio.gatk_glftrio.intersection.annotated.filtered.chr1.vcf", "", "1f3d118dcee9b711714856639930694d"); }
@Test public void uniqueSNPs() { combine2("pilot2.snps.vcf4.genotypes.vcf", "yri.trio.gatk_glftrio.intersection.annotated.filtered.chr1.vcf", "", "ff7bdac468045715d4ac0309d8736c23"); }
@Test public void threeWayWithRefs() {
WalkerTestSpec spec = new WalkerTestSpec(